Difference between manual installations and hombrew installed apps

[SDJeff]

Hi,

i switch to a new Mac M2 from Pro 2020. At the old one i installed several apps manually with the DMG Files.
For example TablePlus. The settings are backuped by mackup in my iCloud drive.

On the new mac i installed a lot by a brew script. After i restored the settings with mackup a lot was running. But for example the Connections in TablePlus or Keyboard Shortcuts of Raycast and also Connections in Transmit are not restored.

Is there a difference in the pathes for the settings? Any ideas or experiences here?